Full disclosure : When I installed it, it did not start up automatically since port 8088 was being used by a Jetty server so I changed the Wowza port to 9099 and then it started up no problem. (If that gives any clues)

Be sure you are trying to transcode a live stream as the Wowza Transcoder does not support VOD transcoding.

If the Transcoder AddOn options does not show up for a live application, please restart Wowza and take a screen shot of the AddOn missing from the Engine Manager. Zip up your /conf, /logs and /transcoder folders and send them to support@wowza.com to open a ticket.